Contacts of the helix formed by residues 192 - 198 (chain F) in PDB entry 1GUL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 192 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190F ASN 3.2 7.8 - - - +
191F ILE* 1.3 95.1 - - + +
193F THR* 1.3 57.9 + - + +
195F LYS* 3.5 9.4 - - + +
196F ARG* 2.8 52.9 + - - +
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Residues in contact with THR 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ALA* 3.2 26.7 - - - +
25F ALA 3.0 22.2 + - - +
26F ALA 4.8 0.4 - - - -
27F GLY* 3.9 14.4 - - - -
191F ILE* 3.6 10.5 - - + +
192F PRO* 1.3 74.9 - - + +
194F ILE* 1.3 71.1 + - - +
196F ARG* 3.2 27.8 + - - +
197F PHE* 2.9 27.8 + - - +
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Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TRP* 4.1 12.3 - - + -
25F ALA* 4.1 23.3 - - + +
153F LEU* 4.9 10.8 - - + -
158F VAL* 5.5 4.0 - - + -
161F LEU* 3.9 22.9 - - + -
188F LEU* 3.5 27.4 - - + +
189F SER* 3.9 3.6 - - - -
191F ILE* 2.8 23.5 + - + +
193F THR* 1.3 89.7 + - - +
195F LYS* 1.3 67.2 + - - +
197F PHE* 3.0 6.9 + - + +
198F LEU* 2.8 41.7 + - + +
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Residues in contact with LYS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F SER 3.5 16.4 + - - +
190F ASN* 4.1 24.2 - - + +
191F ILE 2.3 31.8 + - - +
192F PRO* 3.5 10.5 - - + +
194F ILE* 1.3 69.3 - - - +
196F ARG* 1.3 61.9 + - + +
198F LEU* 3.3 6.5 + - - +
199F GLU* 3.1 43.7 + - + +
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Residues in contact with ARG 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27F GLY* 5.4 3.4 - - - -
192F PRO* 2.8 37.8 + - - +
193F THR* 3.6 28.3 - - - +
195F LYS* 1.3 75.8 - - + +
197F PHE* 1.3 61.6 + - - +
199F GLU* 2.9 40.9 + - - +
200F PRO 4.9 1.2 - - - +
202F SER* 3.8 5.1 - - - -
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Residues in contact with PHE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F GLU* 4.1 3.6 - - - -
20F ARG* 4.0 22.7 - - + -
21F TRP* 3.4 54.1 - + - -
24F ALA* 3.2 31.9 - - + -
30F PHE* 5.2 2.2 - + - -
193F THR 2.9 13.9 + - - +
194F ILE* 3.0 11.8 + - + +
196F ARG* 1.3 76.5 - - - +
198F LEU* 1.3 61.3 + - - +
202F SER* 2.6 33.4 + - - -
203F LYS* 4.0 6.5 - - + -
204F LYS* 3.2 58.5 - - + +
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Residues in contact with LEU 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F TRP* 3.9 15.3 - - + -
165F LEU* 4.1 15.9 - - + -
189F SER* 3.6 35.0 - - - +
194F ILE* 2.8 30.8 + - + +
195F LYS* 3.5 5.6 - - - +
197F PHE* 1.3 80.6 - - - +
199F GLU* 1.3 60.9 + - + +
200F PRO* 4.2 2.1 - - - +
204F LYS* 3.8 28.3 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il